chr22-38140854-C-T
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003560.4(PLA2G6):c.610-685G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003560.4 intron
Scores
Clinical Significance
Conservation
Publications
- neurodegeneration with brain iron accumulation 2AInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Ambry Genetics, Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae)
- neurodegeneration with brain iron accumulation 2BInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
- PLA2G6-associated neurodegenerationInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- autosomal recessive Parkinson disease 14Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151916Hom.: 0 Cov.: 31 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 508Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 274
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74284 show subpopulations
Age Distribution
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at